Add ISM functions and update tutorial #29
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avantikalal
requested changes
Jul 29, 2024
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| Args: | ||
| ism (np.ndarray): The ISM array | ||
| scan (pd.DataFrame): The motif scan DataFrame |
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Let's specify which functions create ism and scan
| rolling_max_ism = _moving_average(max_ism, n=rolling_buffer) | ||
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| # Create plot | ||
| plt.figure(figsize=(10, 4), dpi=200) |
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Can we implement this in plotnine for consistency with the rest of the package?
| @@ -317,3 +317,19 @@ def compare_motifs( | |||
| scan["foldChange"] = scan.alt / scan.ref | |||
| scan = scan.sort_values("foldChange").reset_index(drop=True) | |||
| return scan | |||
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| def calculate_ism_weight(row: pd.Series, ism: np.ndarray) -> float: | |||
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Currently, we average the ISM values over the motif without accounting for whether the shape of the ISM signal (i.e. relative score of different nucleotides at the position) matches that of the motif. Wouldn't it be better if we convolved the ISM matrix with the motif matrix - e.g. using np.convolve or scipy.signal.convolve?
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This pull request adds ISM scoring to motifs.
Updated
src/grelu/interpret/motifs.py:calculate_ism_weightfunction to compute ISM weights across the scan motif DataFrame.Updated
src/grelu/visualize.py:_moving_averagefunction for calculating moving averages of arrays.plot_motifs_on_ismfunction to visualize motifs on ISM data.Updated
docs/tutorials/5_variant.ipynb:Potential todo: draw motif logos on plot.
Testing: